openocd - on-chip debugging, in-system programming and boundary-scan testing tool
binwalk - Binwalk is a tool for searching a given binary image for embedded files and executable code. 
screen - virtual terminal - useful for dealing with serial/uart
minicom - It is used to talk to external RS-232 devices such as mobile phones, routers, and serial console ports.
https://github.com/cyphunk/JTAGenum - enumerate jtag pins
WiringPi-Python python library - An implementation of most of the Arduino Wiring functions for the Raspberry Pi.
i2ctools - a bus probing tool, a chip dumper, register-level SMBus access helpers, EEPROM decoding scripts, EEPROM programming tools, and a python module for SMBus access.
flashrom - read & write external flash memory of the target device which uses SPI communication interface.
avrdude - utility to download/upload/manipulate the ROM and EEPROM contents of AVR microcontrollers using the in-system programming technique (ISP).

http://darkswarm.org/eeprog-0.7.6-tear5.tar.gz - eeprog to read and write to the EEPROM


sigrok-cli & Pulseview - logic analyzer software
https://github.com/richardghirst/Panalyzer - logic analyzer